Introduction

This page provides up-to-date information, documents, reports, and links about the PACS instrument, from preparing observations, through reducing and calibrating PACS observations, to working with PACS maps and cubes.

SPG 14.2.2 products have been generated. This was the final bulk processing of PACS data, fixing the following issues with the previous version:

the Level 2.5 for all unchopped range scans: previously the Level 2.5 were created incorrectly

the Level 3 for all chop-nod pointed range scans: this is being done to have a correct "ObservationSummary" included in the observation dataset, however the data themselves will be no different as the has not changed

HIPE 15.0.1 has been released. There are almost no differences in the data reduction software compared to HIPE 14.2:

for the spectroscopy interactive pipeline scripts, one task has been added which changes the values of two meta data: centreRaDecMetaData, which sets the "ra" and "dec" meta data to the centre of the cube's field for each cube created, independently; it does not change the data or coordinates of the cubes.

new aperture corrections have been added to the calibration tree (photometry), for the prime and parallel modes at the 20 and 60 arcsec/s speeds; the difference in the corrections wrt previous versions (where only the 20arcsec/s corrections were provided) are negligible for apertures of 2*FWHM (of the beam) but larger for smaller apertures.

additional documentation has been added to the PDRG for photometry on extracting uncertainties from scan maps (chp. 4)

the PACS Products Explained includes information about which files to grab directly from HSA tarball downloads (rather than via HIPE), and has a new short chapter on recommendations for different science cases

There are minor updates in the documentation and useful scripts between HIPE 15.0 and 15.0.1, to reflect the recommendations in the PACS Handbook and to link to since-then released documentation.

Due to a bug fixed in the 6.4.4 Unimap release within 14.2.1, the values of some Unimap parameters were modified for a small set of observations in the SPG 14.2.1 processing.

The forward modelling tool (FMT). This tool is to be used with PACS spectroscopy observations of objects which are extended but not flat over the observed field. It is to be used to estimate the correction to the fluxes necessary to account for the uneven illumination of the FoV by the PACS integral field unit (i.e. the gaps between the spaxels). See the Data Reduction section for more information.

Observing with PACS

The relevant documentation to read before working on PACS data for the first time are the following:

PACS calibration and performance

Photometer calibration in scan maps

Point Spread Function/Encircled Energy Fraction :PACS Photometer Point Spread function (10 Mb), version 2.2, 16 November 2015. A detailed document of the in-flight observed PSF and of the derivation of the EEF curves. The accompanying TAR file can be downloaded here (79 MB). It contains the Vesta PSFs FITS files and the EEF tables for all the scanning modes.

Herschel/PACS modelled point spread functions (3.1 Mb) is a related document presenting Zemax modelled point spread functions for both an `ideal' and an 'as built' Herschel telescope model. Tarballs with corresponding broad-band and monochromatic PSFs for these two cases are at http://pacs.ster.kuleuven.ac.be/pubtool/PSF. These are useful in addition to the observed PSFs but cannot replace them, since the models do not capture all effects found in the observed PSFs.

Point-source photometry: PACS uses 5 stars as primary calibrators with fluxes ranging from 0.6 to 15 Jy, plus fainter stars and asteroids as secondary calibrators. The absolute flux scale accuracy is dominated by the model uncertainties and amounts to 5% in the 3 filter bands. At the same time, the reproducibility for a given non-variable point source is better than 2% for all PACS bands. The flux calibration is described in detail in Balog et al, 2013, Experimental Astronomy and confirmed with asteroids in Müller et al., 2013, Experimental Astronomy.

Point-source photometry in deep PACS maps/surveys: The effect of the high-pass filter data reduction technique on the PACS Photometer PSF, point-source photometry, and noise has been investigated in depth in this technical note.

We refer to the paper , G. Aniano et al. (2011) for kernels and associated routines (IDL) to match spatial resolution between several infrared instruments PSFs (PACS, SPIRE, Spitzer/MIPS, Spitzer/IRAC, WISE) as well as GALEX (UV) and other PSF families (gaussian, bi-gaussian, Moffat)

Chop/nod observations:

Chop/nod observations were not used for scientific observations during the mission, however they were heavily used for the photometry monitoring and well as numerous observations for the pointing accuracy check/monitoring. See Nielbock et al., 2013, Experimental Astronomy for the time dependent flux calibration for the PACS chopped point-source photometry AOT mode.

Photometer map-makers

Four fundamentally different map-makers are offered in HIPE 14 with interactive pipeline scripts, starting from Level 1. These map-makers are used in different ways to generate standard products ("SPG" product) provided by the Herschel Science Archive. High-pass filtering is applied to generate Level2 products, while Level2.5 products are generated by combining pairs of observations acquired in the scan plus cross-scan mode, using the Unimap, JScanam, and High-pass filtering mappers. Level3 products are mosaics of Unimap and Jscanam Level2.5 products that belong to the same sky field and to the same observing program.

Highpass filtering branch, where the bolometer timelines are high-pass filtered to remove the 1/f noise, but at the expense of extended emission.

JScanam, a Java-version of the IDL Scanamorphos map-maker, an IDL map-maker from Hélène Roussel (IAP), with an advanced and powerful destriper for PACS maps

Unimap, a GLS (generalised least square) map-maker from Lorenzo Piazzo ('La Sapienza' University of Rome) running under a free Matlab runtime environment. It performs an advanced pre-processing (calibration blocks detection, deglitching, drift correction, jump detection), it implements the pixel noise compensation into the GLS algorithm and it provides post-processing stages. The runUnimap task is used to invoke the Unimap Matlab routine on the users's computer

MADmap, a GLS (generalised least square) map-maker, a GLS map-maker that is not used anymore in the SPG processing, but it is still available as an interactive script

Highpass filtering provides optimum sensitivity to point-sources while JScanam, Unimap and MadMap mappers all clean the dataset of systematic effects and remove the correlated 1/f noise, preserving at the same time the sky signal over large spatial scales. They are suited for analysing both point sources and extended emission.

If you are using data with SPG v 12 or lower, or reducing data with HIPE 12 or lower, remember that the optical field distortion in not applied at level 1. As a result, external map-makers starting from level 1 have a systematic flux overestimate of 6-7% in the red channel and a lower underestimate (~2%) in the blue channel of the flux scale. From HIPE 13/SPG 13 onwards, this has been corrected.

Links:

Scanamorphos by H. Roussel can be used to build maps from scan observations made with bolometer arrays, in particular with the PACS and SPIRE photometers

PACS spectrometer calibration

The calibration of the spectrometer is based on repeated measurements of planets, asteroids, and stars.

Telescope background model for chop nod: a script to compute the telescope background model calibration tables and a technical note explaining the method used can be found here. Warning: the calibration tables computed with this script are not the same as the ones in the calibration tree. See the technical note for details.

Point source observations. To extract and calibrate the spectrum of a point source, it is necessary to use one of the tasks provided: it is not enough to add up the field-of-view of use the central spaxel only. How to do this is documented in the PACS DRG for spectroscopy.

The absolute flux error of >100 measurements of different calibration sources is ±6-12% in all bands, with a systematic error below ±1%. Continuum flux reproducibility from observations on HD 161796 is estimated at ±15% (peak-to-peak).

An explanation of the data errors for any particular observation is provided in the PACS Data Reduction Guide for spectroscopy (sec. 7.6)

PACS spectrometer beams: The PACS spectrometer beam efficiencies are maps of the response of each detector on the sky. They describe the (relative) coupling of a point source to each spaxel as a function of its (the source) position in the FOV.

Version 6, the most up-to-date, can be directly downloaded as a tar ball PCalSpectrometer_Beam_v6.tar.gz. The calibration files are named BeamsPerSpaxelXXX, depending on the [XXX] band.

The PACS beam efficiencies are based on Neptune raster maps at certain (14) wavelengths observed during the mission:

Fine Neptune 5x5 raster maps with raster step size 2” were executed on ODs 1311 and 1312. The combination of four such fine rasters, offset by 1", provide very high sampling but for the central spaxel beam efficiency only.

All these measurements were registered using least squares minimisation in coordinates and gain, and a synthetic beam was constructed with the coarse raster outside the area covered by fine raster and from matched fine raster inside. Finally, this synthetic beam is interpolated into a 0.5" grid.

All raster maps were observed with only one chop-off position (aka, asymmetric chopNod).

Beam efficiencies are normalised so that a point source of flux 1 at the centre of spaxel 12 has an integral of the instrument response equal to 1.

The WCS associated with the beam is in sky coordinates for position angle 0.

The raw data from which the PACS spectrometer beams (all versions) were derived are also available as tables (y, z offset - signal):

SpecSpatial_BeamEfficiency_central_spaxel_tables_v1.tar.gz: This contains a FITS file for each wavelength measured for the central spaxel only. Raw data of the coarse and fine rasters are combined. The array dimension of the fits file is [3,npoints] where the first column gives the y raster position, the 2nd column the z raster position and the 3rd column the normalised flux measured at this raster position.

SpecSpatial_BeamEfficiency_tables_v1.tar.gz: Raw measurements PACS beams - all spaxels, coarse raster measurements only: each fits files corresponds to one wavelength. Each file contains the data for all spaxels of the coarse raster measurement only. Each fits file holds an array of 3x25x25x25 where: (0,25,25,25)=y raster position, (1,25,25,25)=z raster position, (2,25,25,25)=flux normalised to the central spaxel. The second and third dimensions are the raster position indices (y and z) and the last dimension is the module number (=spaxel number).

PACS calibration file versions

When starting HIPE, you will be informed if new calibration files are available. Clicking on show details will show you the release note of the new calibration set, with details about the changes. This is further explained in the PDRGs. Clicking on Install will install the latest calibration files.

You can inspect the release notes for the calibration sets installed on your machine from within HIPE. Open the Calibration Sets View from the menu Window -> Show Views -> Workbench.

The history of the calibration files that have been released to the community is provided here: PACS Calibration File History. With the release of HIPE 15 and the final SPG processing of 14.2, no more changes to the calibration tree will be made.

Reducing PACS data

Standard Products

All observations will be processed to Level 2. The pointed chop-nod observations for which the full SED is covered by 2 (or more) observations will also have a Level 3 (see for a list of these observations). The unchopped range scan on-source observations for which an off-source observation was requested will have a Level 2.5 that contains the background-subtracted results (see for a list of these observations, and the associated off-source obsid for any on-source obsid is given in the comments in the qualitySummary).

For some observations, one of the cameras (red or blue) may not have processed all the way to the final level due to data being out of the filter band borders: this is normal and a comment in the qualitySummary should say exactly that. Some observations will have failed in one camera but not another due to instrumental anomalies: again, a comment in the qualitySummary will explain what has happened.

This Data Processing Known Issues page describes typical problems and caveats the observer needs to be familiar when looking at the results of this "SPG" (standard product generation) processing. Aspects of product quality which can be further optimised by interactive processing are also summarised here. The document refers to the version of data processing pipeline currently being used for processing of incoming Herschel data.

For a explanation of PACS products, i.e. what you get when you download a complete or part of an observation from the HSA, see the PACS Products Explained, which can also be found on the HIPE help pages.

PACS data are reduced with pipeline scripts which are a set of command-line tasks that process the data from Level 0 (raw) to Level 2/2.5 (science-ready). There is more than one flavour of pipeline script, tailored to different types of science target, AOT, and observing plan. These 'interactive' pipeline scripts are provided in HIPE and explained in the data reduction guides.

The data you get from the the HSA will have been processed by the 'SPG' (Standard Product Generator) using one pipeline script flavour per AOT. Which script is used is documented in the PDRG.

The SPG scripts include all the stable pipeline tasks within those scripts, with task settings that correspond to the most common type of science target for each AOT. But some pipeline tasks still can only be run via the interactive pipeline scripts, and to modify the parameter settings for the important pipeline tasks also requires you re-process the data. The Launch Pads (see below) include a guide to understanding the pipeline scripts and how to decide whether to reprocess your data and if so, with which script.

AOT table for PACS spectroscopy

For any user of PACS data, it is necessary to have some information about the AOT -- the observing mode -- of the observation they are working on in order to know which of the SPG products to work with, which pipelines to use, and which calibration or other uncertainties to consider. All the relevant AOT details are held in the header keywords of the FITS files. Every FITS file in an HSA download has a complete copy of the keywords, and hence any Level >=2 product can be opened (e.g. in fv) to find the AOT. Tables containing the description of the AOT keywords can be found in the PACS Products Explained.

For photometry, almost all observations were of the scan-map mode and hence the same set of three maps are provided, where the key to knowing which to use is in the final chapter of the PACS Products Explained. For spectroscopy there were may more variations on the AOT: pointing mode, spectral mode, background sampling, type of mapping. In addition, the Level 2 and 2.5 products for spectroscopy are "sliced": each cube or table is for one wavelength range only, and the filenames differ only by an "s##" where more than one wavelength range was requested for that observation. This is also explained in the PACS Products Explained. In order to make it easier for an archive user to know, before having to open any FITS file, which FITS file they want, we have created a spreadsheet of AOT keyword data. In this tarball (spreadsheet/readme), you will find: the obsid; line/range spectroscopy; chop-nod or unchopped; pointed or mapping; if mapping, the raster details; the number of spectral lines or ranges requested or "sedxxx" to indicate that the observation is a full SED in the xxx band; line IDs given by the observer; and then four columns of slice number (the "s##" in the filename) and wavelength range: two columns (red and blue camera) for pointed observations where the search was done on the rebinned cube (one of the final products for this mode), and two columns (red and blue) for mapping observations where the search was done on the projected cubes (one of the final products for this mode).

All standard observations that processed to at least Level 2 in the SPG pipeline are included in this table.

Data reduction: HIPE, documentation, and useful links for data issues

HIPE (Herschel Interactive Processing Environment) is the tool used to inspect, reduce, and analyse Herschel data.

The recommended User Release HCSS (Herschel common science system) version that you should use for reducing PACS data is HIPE v15.0.1

Within HIPE you can access all the PACS data reduction documentation and the general HCSS and HIPE user documentation for Track 15.0.1 here. The documentation provided via HIPE opens in a web browser, but for those of you who prefer PDF, we include the PACS Data Reduction Guides as PDF files here (note that within the standalone pdf versions, external links will not work):

For HIPE 15(.0.1) go to the HIPE 15 (all tracks) what's new page. Note that no bulk processing will be done with this HIPE release and the pipeline scripts are no different to those of HIPE 14, the only difference wrt HIPE 14.2.1 are some useful scripts and documentation improvements.

The Data products known issues page details issues about the pipelines or the data products that are known about and offers advice for dealing with them. Consult this if you encounter problems with your data to see if it has already been addressed.

FMT (forward modelling tool).
Some information about this is provided in the spectroscopy PACS Data Reduction Guide. A quick summary is:

the FoV of the PACS integral field unit is not uniformly illuminated, which leads to some loss of light between the spaxels

for point sources and flat sources this does not matter -- the corrections applied by the pipeline (the point source corrections in extractCentralSpectrum, for example, and the extended source correction applied to all observations by the pipeline) account for this

for sources that are between a point and fully extended, for crowded fields, and for off-centred point sources, however, the fluxes in the final cubes of the pipeline will be incorrect

The FMT has been developed in HIPE 15 to estimate the degree to which the fluxes are incorrect for any observation. As this differs for each observation -- it depends on the surface brightness distribution of the source and the pointing pattern of the observation (pointed, Nyquist mapping, oversampled mapping, tiling...) -- the correction is unique to each observation. To use the FMT it will be necessary to run HIPE. The most important input is a model of the surface brightness distribution of your source at the wavelength(s) of the observation. With this input, the surface brightness distribution that would have been observed with a completely uniform illumination is estimated by running the pipeline on the model. This output can be compared to your data.

The FMT functionality is fully incorporated in HIPE 15, however it has not yet been tested on general users, and for this reason we recommend you to contact the Herschel helpdesk to ask for advice on running the code. In exchange for some one-on-one help, we would appreciate feedback on the scripts and the documentation provided in the FMT package.

Interactive pipeline scripts

The various interactive pipeline scripts PACS photometry and spectroscopy provide in HIPE can be seen as cookbooks, since they take you through each pipeline, task by task, explaining briefly what each task does, commenting on the more crucial pipeline tasks, and showing you how to plot, image, visualise and inspect your data as you work through the pipeline. An example public observation is included with each so you can test it out before using it on your data. These data reduction scripts are available in HIPE under the menu: Pipeline --> PACS --> Photometer/Spectrometer.

The PACS Launch Pads are taken from the first chapters of the respective PDRGs and are a useful quick-start guide to loading your data into HIPE, looking at them, and then what to know and do before you begin reprocessing your data with one of the pipelines. These can be gotten via HIPE itself or the links here (these are to the HIPE 15 versions, which are the same as the HIPE 14 versions)

HIPE Academy on YouTube: here you can find recordings of various seminars and webinars that the HSC have given on working in HIPE, reducing Herschel data, using various tools to visualise and manipulate data in HIPE, and etc.

Quick links: wavelengths, sensitivity, PSFs

A summary of instrumental and calibration details that a data-reducing astronomer often wants know.

Spectroscopy

Wavelength ranges, resolution, band names

The blue bands are B2A (blue, second order) and B2B (green, second order), and B3A (blue, third order), and in the red we have R1 (first order)

Second-pass spectral ghosts: see sec. 4.2 of the PACS Spectrometer Calibration Document to learn about ghosts. These are bright spectral lines at one wavelength "echoing" to another wavelength in another spaxel. This is also documented in sec. 4.9 of the PACS Observer's Manual * The footprint of the integral field unit: text and figures showing the footprint of the PACS IFU, and how that compares to the beam, can be found in the PACS Spectrometer Calibration Document (sec. 3) where you will also find information about the beam maps (at high spatial resolution and for various wavelengths), beam efficiencies, and the point source loss corrections. The same information can be found in the PACS Observer's Manual (sec. 4.6).

Spectral line profile skews for off-centred sources: point sources that are not centrally located in a spaxel will show a skew to their spectral lines. The effect of this is to move the peak wavelength and slightly change the measured FWHM. Some calibration of this has been done and this can be found in sec. 4.7.2 and 4.7.3 of the PACS Observer's Manual and sec. 5.2 of the PACS Spectrometer Calibration Document.

Expected signal-to-noise ratios and line sensitivity: this depends on the AOT, this information is also provided in the AOT Release Notes (see also update in sec. 6.1.3 of the PACS Observer's Manual) and can also be computed by running HSPOT.

Photometry

Filters and bands

The blue and green bands are not observed simultaneously, the red is observed simultaneously with each. Transmission functions can be found in the PACS Observer's Manual sec. 3.2.

PSF and beams: the beams maps are provided as FITS files, and information about then can be found in the section 'Photometer calibration in scan maps'

Point source photometry

Colour corrections: these are provided on this page in the section 'Photometer calibration in scan maps'

Aperture corrections/EEFs (encircled energy fractions) are provided in sec. 8 of the PACS Photometer Point Spread function document. See the section 'Photometer calibration in scan maps' on this page.